


Peter Parker, Agent of SHIELD

by Missellaineous



Category: Deadpool - All Media Types, Spider-Man - All Media Types
Genre: Aftermath of Torture, Angst with a Happy Ending, Canonical Character Death, Fluff, I don't read comic books, I'll tag more things as I finish writing the rest, M/M, Other, Strippers & Strip Clubs, Torture, Unresolved Sexual Tension, but it does get a little warm later, don't even ask me how much research I did, it takes a while to get there though, slowburn, spoilers are in the tags
Language: English
Status: In-Progress
Published: 2020-07-27
Updated: 2020-07-27
Packaged: 2021-03-05 03:21:47
Rating: Mature
Warnings: Graphic Depictions Of Violence
Chapters: 1
Words: 3,779
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/25027630
Author URL: https://archiveofourown.org/users/Missellaineous/pseuds/Missellaineous
Summary: Death changes Peter’s life four times.After Gwen dies, Peter gives up being Spider-Man. During his graduation ceremony, he’s approached by a SHIELD agent with an offer he finds incredibly tempting. Once he accepts, he has to endure tough training, run-ins with insane mercenaries, and fights with a revived Nazi organization with suspicious ties to his past.
Relationships: Clint Barton/Phil Coulson, Past Peter Parker/Gwen Stacy - Relationship, Peter Parker/Wade Wilson
Comments: 4
Kudos: 22





	Peter Parker, Agent of SHIELD

**Author's Note:**

> No, this has nothing to do with The Amazing Spider-Man movies. I mean if you want to imagine Garfield's Peter when reading this then go for it, I encourage people to picture their favorite Peter. But I haven't even seen the second movie, and it wasn't the inspiration for this story in any way. Peter is graduating from college with his Master's degree, not from high school. He's 24 at the start of this fic (21 in the opening scene). I prefer to take elements from several different versions of Spider-Man, and I wanted to say this because I didn't want to mislead anyone. It's the reason why I tagged this all Spider-Man-All Media Types in the fandom tags.  
> I'm frankensteining stuff from all kinds of spider-man media, so while I wouldn't claim that any of this is particularly original, it's my personal take on what could have happened to this version of Peter Parker. Considering how often canon changes stuff up I don't really feel bad for doing whatever I want with Peter. I'm not tagging Agents of SHIELD or the MCU because this doesn't use much from those even if I borrow some of the characters. My goal is to make this fic accessible to everyone while giving people who are at least as familiar as I am with spiderlore some things to point and go "hey look it's _______".  
> So come one, come all! Let's just have fun with it.  
> I made a playlist if you wanted to listen to something while reading:  
> [youtube playlist](https://www.youtube.com/playlist?list=PLwPtTKrdStSuWgTi-0GbEYG9UmUM1wYY5)  
> [spotify playlist](https://open.spotify.com/playlist/6jwTXOAiTPhTqEEpJ071m3?si=k8Q5V1MSQBe1H8oUuAtalQ)  
> Text dividers made by [this talented person](https://whimsicalrogers.tumblr.com/) and [this other talented person](https://writeyourmindaway.tumblr.com/)

Peter walked into his house through the front door, too exhausted to sneak in through his bedroom window like usual. He’d barely had the energy to pull a sweater and jeans over his spider suit after the fight. His backpack hung from one hand and his mask was balled up in the other. He found Aunt May in the kitchen getting a late-night snack. She smiled when she saw him.

“Peter, I didn’t know that you had gone out. Were you on a date with Gwen?”

Peter dropped his things and stepped forward. He wrapped his arms tightly around his aunt and buried his face in her shoulder. He had to bend down to do it, but she smelled like home. She immediately started running a hand up and down his back. “Are you alright? Did something happen?”

Her kindness broke through the last of his composure, and Peter started sobbing uncontrollably. May hushed him as she held him. She waited until he’d cried himself out, then she sat him in a chair and made him drink some water.

“Tell me what’s wrong, hun. What’s got you so worked up?”

“I-“ Peter’s voice broke. He swallowed and tried again. “I killed her.”

“What are you talking about?” She sounded so confused.

Peter started tearing up again. “I ki-killed Gwen.”

May sat down across from him, her expression serious. “I think it’s best you tell me everything that happened.”

So Peter did. Everything he’d been holding back for years spilled out once he started talking. He told her about getting his powers, cage fighting for money, his role in Uncle Ben’s death, becoming Spider-Man, everything that happened with the Osborne’s. His voice was so hoarse by the time he caught up to the present that May had to get him another cup of water and a cough drop. She listened without interruption until he was finished. “And now, I don’t know what to do. Gwen is- Gwen is dead because of me.”

“I see.” His aunt stood up and circled around the table so she could hold him and press a kiss to the top of his head. Peter pressed his face into her stomach. “You’ve been working so hard, baby. You’re definitely a Parker, always trying to save everyone else.”

Peter sighed. All he could think about was Gwen’s face when he had her in his arms for the last time. Her eyes had been closed, like she was just sleeping. He wished more than anything that he’d been the one sleeping, that it had all been a nightmare. If he couldn’t even save Gwen, what was he supposed to do?

“All right, then. You just leave it to me.”

Peter pulled back and looked up at her. She pushed his hair out of his face. “What do you mean?”

“Don’t you worry about it. I’ll take care of everything. I want you to go take a shower, and when you’re done come to the living room.”

“But, Aunt May-“

“Nope. All I want to hear out of you is a ‘yes, ma’am’.”

He nodded reluctantly. “Yes, ma’am.”

“Good. Go on, now.”

Peter slowly made his way up the stairs and into the bathroom. Distantly, he could hear Aunt May talking on the phone, but he didn’t bother to listen. He turned the knobs, and the rushing water worked as white noise to drown out the rest of the world.

He’s not exactly sure how long he was in the shower, but there wasn’t any hot water left by the end, and his skin felt raw and sensitive from being under the hard water pressure for so long. When he got to the living room he found May sitting on the couch and watching a late night tv show with the volume turned low. She noticed him standing in the doorway. “Come here, Peter.”

She pulled him down until he was leaning against her, his head pillowed on her shoulder.

“Are you hungry?”

Peter shook his head.

“Let me know if you change your mind.”

Peter nodded and closed his eyes. He fell asleep pressed against her.

**  
**

**-Three Years Later-**

  
It took ages for Peter’s name to be called, but May had been so excited to take pictures of him graduating that Peter had to participate. He made sure to wave at her as he crossed the stage. The rest of the ceremony dragged, but it was over soon enough. He was making his way through the crowd to Aunt May when a woman in a business suit approached him.

“Peter Parker, it’s nice to meet you.” She held out a hand, and her grip was firm when he took it. The contact between them sent a shiver through Peter, and something about her felt familiar even though he was sure he’d never seen her before. He resisted the urge to put his hands in his pockets after she let go.

“You too, miss…?”

“Jessica Drew, agent of SHIELD. We’ve had our eyes on you for quite a while, Mr. Parker. We think you could do great things if you joined our organization.”

He wasn’t sure what to say. He didn’t want to tell her that he’d never heard of SHIELD before. “Oh, uh…”

Agent Drew gave him a knowing smile. “I understand this is rather sudden. Here.” She handed him a business card. “Think about it and call us if you’d like to know more. We’d love to hear from you, Mr. Parker.”

She walked away, and a guy walked by and punched Peter on the shoulder. “Dude, she’s hot! Nice one!”

Peter ignored him and tucked the card into a pocket. It took a minute to locate May in the chaos of the crowd. She tackle-hugged him as soon as he was in range. “Oh, Peter, you looked so handsome! Come here and stand against the wall so I can get some more pictures of you.”

She’d brought the old camera he’d gotten for his job at the Daily Bugle and took at least a dozen pictures of him, until a kind stranger offered to take a few of them together. When May was finally satisfied that she had properly documented the event, they left to get an early dinner at their favorite Thai restaurant. It was just a little hole in the wall joint, so it wasn’t as crowded as most of the other places in the city.

“I’m so proud of you, Peter. It takes a lot of hard work to get a college degree, especially with everything you’ve gone through. And you’re going to do even more amazing things, I just know it.” She patted his hand.

“Thanks, Aunt May. I couldn’t have done it without you and Uncle Ben. I owe everything to you.”

Her eyes softened and she smiled. “You’re a good boy, Peter, and I’m sure your uncle would be just as proud as I am, if not more. I bet you’re excited to start working soon. Have you sent out any applications yet?”

Peter took a bite of his food. “Uh, kinda. A recruiter actually came up to me earlier.”

She clapped excitedly. “That’s great news! Do you think you’ll go for it or hold out for something else?”

“I’m not sure. I guess I’ll call them and see what their offer is before I decide.”

She pointed her fork at him. “Smart. Make sure you know what you’re signing up for before you sign anything. You should always read the fine print.”

He nodded since his mouth was full.

“You're gonna set the world on fire, hun. I just know it.”

After two weeks of waffling back and forth, he finally called them. The man on the phone scheduled an interview for him at a downtown office the next day. When it was time, Aunt May kissed him on the cheek and wished him good luck. He barely made it there in time after stopping twice on the way-once to help an older woman with her bags, and a second time to buy a homeless man a sandwich.

A non-descript man in a suit greeted him when he went in. “It’s nice to meet you, Mr. Parker. I’m Agent Coulson.”

“Nice to meet you, too.” Peter shook the man’s hand.

“I’ll be the one conducting your interview. If you’ll follow me, I’ve got a conference room set up.”

Peter followed him down the hall and walked through the door Coulson held open for him. He sat in the chair closest to the window. Coulson sat down across from him. “Do you need anything before we start? There’s a couple of vending machines around the corner.”

“I’m good, thanks.” He tapped the knuckle of his thumb against the tabletop anxiously.

“Then we’ll get started.” He pulled a file from out of nowhere and flipped it open. “Spider-Man.”

Peter flinched.

“You protected New York City for seven years and patrolled the streets almost every night. And then, three years ago, you stopped. A lot of people think you died. The rest think you abandoned them. Considering the circumstances of your last fight, it’s easy to understand the reason for your…let’s call it early retirement.”

He laid out several pictures. Peter looked down at them and saw shots of himself fighting Green Goblin, swinging between buildings, and one picture of Gwen. She was smiling and pushing back her hair behind one ear. It made his heart ache to see her, even if it was just a photo. He looked up to see Coulson watching him. He swallowed.

“I’m not sure what this has to do with the interview.”

“Simply put, we think you have the makings to be a great agent. You have a unique skillset.”

Oh. “What kind of agent?”

“I think you’d be quite good at infiltration, personally. But we wouldn’t decide what your specialty would be until after negotiating your contract and putting you through our training academy.”

Peter blinked. “You want me to be a spy?”

“You’ve got a lot of potential, anyway. You’ve got the face for it-brown hair and eyes, no defining features, and you’re of average height. You could maintain anonymity fairly well. With training you could be one of our best. We do have a second offer, if you want to hear it.”

“Yeah, I think that would be good,” Peter said weakly. “To hear it, I mean.”

“Well, you’re more than qualified to join our science division. If you worked for us, we’d fund your doctorate program for one, and we’ve got the third largest electron microscope on the eastern seaboard. Plus, if you joined SHIELD you would get access to samples you could never touch if you worked anywhere else. We work with several other organizations to…contextualize previously undiscovered phenomena they aren’t equipped to handle.”

“What does that mean?”

“It means we deal with the weird stuff no one else knows what to do with. Giant green monsters rampaging through Harlem, aliens, magic-“

“Radioactive spiders?”

That made Coulson smile. “Some things slip through the cracks, but we have a good team and the best resources. Who do you think handled the cover story for the last incident with Green Goblin?”

That baffled Peter, because he had been sure that the coverup had been Harry’s doing, or a result of Norman’s will or something.

“Not a lot of people get an offer like this, but as I said, you’re rather unique, Mr. Parker. I have no doubt you would excel in either position.”

Peter sat there for a minute while his mind worked. He had been thinking about trying for a doctorate in chemical engineering, and if Coulson was telling the truth about having opportunities no one else did, then this would be the chance of a lifetime. Before he decided anything, though, he needed more information. “What exactly would I be doing, if I were a spy?”

Coulson seemed satisfied with the question. “Something you’re very familiar with-fighting crime. Most of your missions would probably be intelligence gathering or asset retrieval. There’ll be plenty of travel, including overseas. You could also go undercover, be part of a strike team. Occasionally we run protection details for high risk victims who fall within our jurisdiction. It depends on how your training progresses, and on what you want to accomplish while you’re with us.”

Peter frowned. “What are the conditions?”

“You’d spend at least two months in one of our training facilities, to start with. You’ll have a minimum of three days off in between missions, unless there’s an emergency. You will receive a monthly salary, and an excellent insurance package if I do say so myself. Everything else you’d need to know is detailed in this contract.”

Coulson slid a packet of papers toward him, and he started flipping through it, glancing over everything. “Do you have any questions?”

“Yeah, actually. How do I know someone won’t go after my aunt? If I use my powers on missions, it won’t be long until someone connects me to Spider-Man. I’m lucky you guys were the only ones who bothered to look as closely as you did. I’m really not interested in putting May in any more danger than I already have. That’s why I put up my suit.” He gingerly touched the edge of one of the photographs and straightened it while avoiding looking at it closely.

Agent Coulson nodded at the papers. “Page three. You’ll have the option of using an alias, and you’ll be given a codename while you’re on a mission. Only a few officials will know your true identity-your trainer, your handler, the director, and me. It’s nothing we haven’t done before for other agents. You’re not the only one who has a family they want to keep safe. Any files concerning civilian families are only kept on paper in a secure location just in case someone gets past our computer firewalls. We only have them in the first place for insurance reasons. As far as your concerns with being connected to Spider-Man go, we think that not using your webs will go a long way toward keeping your alter egos separate. As long as you don’t crawl on walls in front of everyone, there shouldn’t be a problem.”

Peter nodded. It all seemed pretty reasonable, but he was still reeling from the unexpected direction of the meeting, so who was he to tell? “I’d want to keep my aunt informed as much as possible.”

“I’m sure that can be arranged, as long as you don’t share any confidential information.”

“Okay.” He sat back in his chair and ran a hand through his hair. “Can I have a couple days to think about it?”

“We’d like a response within the next five days, whether or not you accept one of our offers. Take the contract with you. Look it over, have a lawyer check it out, whatever you need. Call us if you have any more questions or to let us know what you decide.” Coulson put the photographs back in the folder and stood up. “I’ll escort you out.”

They shook hands again at the door, but Peter felt almost like a he was different person than earlier that morning.

“I look forward to hearing from you,” Coulson said.

Later, when he sat down with May for dinner, she asked him how the interview went. “I can’t remember if you told me what company it was for,” she commented.

“I’m not sure you’ve ever heard of them before. They’re called SHIELD.”

May dropped her fork, and Peter jumped. She was scowling. “SHIELD? That bunch of self-righteous busybodies? What do they want?”

“Uh, to offer me a job. Do you know them? They said they helped cover up the whole thing with Norman and…and you know.” He waved a hand to indicate everything involved with the whole incident. Seeing Gwen’s photograph and having his past brought up suddenly had shaken him, and as much as he didn’t want to talk about it, he had some questions. “Back then, you told me not to worry, that you were going to take care of it. Did you call them to come clean up my mess?”

May sighed and pushed away the rest of her food. She went to the cabinet and pulled out a bottle of whiskey and a couple of shot glasses. Peter was too surprised to say anything while she poured them each a drink. “Those nosy jackasses don’t know when to quit.” She downed her first shot and poured another.

“What?”

May sighed again. “SHIELD contacted your uncle when you were in high school to try to recruit you into their science program. We turned them away because you were just a kid and we didn’t want you to be forced into the same world that killed your parents. We didn’t tell you at first because you were too young, and then we just hoped they’d leave you alone. I should have known better.”

“What are you talking about? Mom and Dad died in a plane crash,” he protested. It was the second time today he felt like his world was turning on him. He felt like he’d been teetering on the edge of something big without realizing, and now he was falling.

“Richard and Mary worked for SHIELD. Didn’t you ever wonder why they left you with us so often when you were little? They were on that plane in the first place because they were running. A lot of people wanted to get their hands on your father’s research, and one of them sabotaged that plane.”

Peter felt like he’d stepped into one of those wacky funhouse mirrors. “My parents…were spies?”

“Maybe I should have told you before. But your parents did everything they could to keep you safe, and we all wanted you to have a normal childhood.” She took another drink. “Then, despite everything, you became a superhero. I thought we’d actually managed to protect you all these years, only to find out that you were in more danger than I could imagine. It’s like fate.” She downed her second shot, and Peter swallowed his first. The alcohol burned through him, but it helped keep him grounded.

He had no idea what to say. He’d spent so long doing everything he could to take care of his aunt. This was a particularly harsh reminder of everything she’d done for him.

She continued, “When you told me the truth about Spider-Man, about everything, I was so proud of you. But I was scared, too. I called SHIELD to help because they owed me a favor, then I stayed up all night looking up all the fights you’d been in. You’ve almost died so many times. I was relieved that you decided to stop. But I should have known it was only temporary.”

Peter took one of May’s hands. “I’ll turn down the job, Aunt May. You don’t have to worry. I’ll stay right here where you can keep an eye on me.”

May shook her head. “I know you want to go. You’re just like your father and uncle. In your heart you’re a hero, Peter. I’d rather you not be alone while you’re trying to save the world. As much as I hate to admit it, joining SHIELD might be your best option.”

“You’re more important,” he said.

“I’ll be fine. I’m not the one who’ll be running straight into danger. You let me be the parent, okay?” She put her other hand on top of his and squeezed. “Do what you think is best. You’re a good man, and I’ll support you no matter what. You’ve got a tough road ahead of you, no matter what choice you make. Don’t try to change just because of an old lady’s worry.” She chuckled.

“Okay,” he croaked. He cleared his throat. “You know, they suggested I use an alias to keep my identity safe. I was thinking of going by Ben, because it’s my middle name and, y’know, for Uncle Ben.”

May smiled. “I think that’s a great idea. Have you decided on a last name?”

“Not yet. I was thinking Peterson, maybe. I want it to be something familiar, but it might be too close to the truth.”

“If you want something familiar, you could use my maiden name,” she suggested.

Peter grinned. “Ben Reilly does sound kinda catchy.”

“Good. Also I’m definitely looking over that contract before you sign it.”

“Deal.”

The rest of his evening was quiet as he thought about what it meant to become a SHIELD agent. After he handed over the copy of the contract he’d been given, he did the dishes while May looked over practically every letter. When the kitchen was cleaned up and Aunt May had gone to bed, he closed his bedroom door before he pulled a box out of the back of his closet. He pulled out all of his old spider-gear. The suit looked the same as always, with a few tears in it he’d never gotten around to mending. He stared into the eyes of the mask for a minute before he looked at the rest. His webshooters were a little dusty, and the cartridges in them were half empty. There were full and empty spares rolling around in the bottom of the box.

Sitting at his computer with his suit in his lap, he could almost pretend that it hadn’t been three years, and that he was up late after sneaking in through his bedroom window trying not to wake his aunt up after spending the evening patrolling the city. He’d spent a lot of time avoiding her and sneaking out behind her back before.

Quitting had been a relief for him in a lot of ways. He was actually able to get a full night’s sleep when he didn’t have nightmares, and he had time to hang out with his friends. Not that he had a lot of those, but still. He did stop the odd purse snatcher, because doing nothing wasn’t an option even if he didn’t go looking for trouble anymore. But he knew, as soon as Agent Coulson had told him what he could be doing, that he was gonna say yes. Even just the thought of getting back out there, of using his powers to help people again, made him feel more alive.

He pulled the mask on for the first time in years and looked at himself in the reflection of his computer monitor. He took it back off after a moment. It would be better working for SHIELD. _He_ would be better.

**Author's Note:**

> Thank you to everyone who leaves kudos and comments, y'all are the heart of the fandom community. Without readers, writers would just be yelling into the void.


End file.
